利用高密度SNP芯片分析杭猪的群体遗传结构

旨在更好地了解杭猪保种群体的遗传多样性、亲缘关系和家系结构，有效保护和利用杭猪遗传资源。本研究使用50K SNP芯片对30头杭猪（4头公猪，26头母猪）保种个体进行了单核苷酸多态性（single nucleotide polymorphism，SNP）测定，通过Plink软件对获得的基因型数据进行质控，用于最小等位基因频率、观察杂合度、期望杂合度和多态信息含量的计算，分析杭猪保种群的遗传多样性；使用Plink计算连续性纯合片段（runs of homozygosity，ROH）、构建状态同源（identity by state，IBS）距离矩阵，并计算得到基于连续性纯合片段的近交系数；采用Gmatrix软件构建G矩阵，分析杭猪保种群的亲缘关系；使用Mega X软件构建公猪进化树，分析保种群体的家系结构。结果表明，30头杭猪共得到57 466个SNPs标记，平均检出率为0.988 3±0.000 4，通过质检SNPs数为34 156；平均最小等位基因频率为0.228±0.137，平均多态信息含量为0.255±0.098；平均观察杂合度为0.359±0.181，平均期望杂合度为0.314±0.140。杭猪保种群体平均IBS遗传距离为0.241 7±0.033 6，公猪平均IBS遗传距离为0.178 3±0.025 5；G矩阵分析结果与IBS距离矩阵一致，两个结果均表明杭猪保种群部分个体之间亲缘关系较近。30头杭猪个体共检测到828个ROHs，83.33%的ROH长度在10 Mb以内，平均长度为（6.96±9.62） Mb，个体ROH平均总长度为（191.95±201.56） Mb。基于ROH的平均近交系数为0.078±0.082，其中公猪平均近交系数为0.219±0.082，说明杭猪保种群整体的近交程度不严重，但公猪存在近交。进化树结果表明，杭猪保种群体目前只有2个家系，其中1个家系包含4头公猪，另一个家系不含公猪。综上所述，杭猪保种场的保种群公猪的血缘数量少，母猪近交程度低，公猪存在近交，需要引入新血统或创建新血统来维持家系结构的平衡以利于杭猪遗传资源的长期保存，防止杭猪遗传多样性的丢失。

Analysis of Population Genetic Structure of Hang Pigs by High Density SNP Chip

The purpose of this study was to better understand the genetic diversity, relationship and family structure of Hang pigs conserved population, protect and utilize the genetic resources of Hang pigs efficiently. The 50K SNP chip was used to detect the single nucleotide polymorphism (SNP) in 30 Hang pigs (4 male and 26 female). And the quality control of SNP genotyping results was conducted by Plink software to calculated the minor allele frequency, observed heterozygosity, expected heterozygosity and polymorphism information content so as to analyze the genetic diversity of Hang pigs conserved population. The runs of homozygosity (ROH) was calculated and identity by state (IBS) distance matrix was constructed by Plink software, the inbreeding coefficient was then calculated based on ROH. The genetic relationship was analyzed according to the G matrix result constructed by Gmatrix software. The boar phylogenetic tree which constructed by Mega X software was used to analyze the family structure of Hang pigs conserved population. The results showed that, 57 466 SNPs were detected in 30 Hang pigs, the average genotyping rate was 0.988 3±0.000 4, there were 34 156 SNPs passing quality control. The average minor allele frequency, polymorphism information content, average observed heterozygosity and average expected heterozygosity were 0.228±0.137, 0.255±0.098, 0.359±0.181 and 0.314±0.140, respectively. The average IBS genetic distance of Hang pigs conserved population and boar were 0.241 7±0.033 6 and 0.178 3±0.025 5, respectively, and the result of G matrix was consistent with IBS genetic distance, the IBS genetic distance and G matrix results showed that some individuals in Hang pigs conserved population were closer to each other. A total of 828 ROHs were detected in 30 Hang pigs, and the length of 83.33% of these ROHs was less than 10 Mb, and the average length was (6.96±9.62) Mb, and the average total length of individual ROH was (191.95±201.56) Mb. The average inbreeding coefficient based on ROH of Hang pigs conserved population and boar were 0.078±0.082 and 0.219±0.082, respectively, indicated that the inbreeding degree of Hang pigs conserved population was not serious, but there was inbreeding in boar. The phylogenetic tree result showed that, there were only two families in Hang pigs conserved population, and one family contained all 4 boars and the other family only contained sows. In summary, the blood number of the boar of conserved population in the Hang pigs conserved farm was few, the inbreeding degree of sow was low, but there was inbreeding in boar, it was necessary to introduce new blood or create new blood to maintain the balance of family structure, so as to facilitate the long-term preservation of Hang pigs genetic resources and prevent the loss of genetic diversity.